Abstract: Aquilaria is a tree species belonging to the Thymeleaceae family. When Aquilaria sp. is injured, it can produce agarwood. Agarwood is characterized by a darker wood colour than the healthy one and by a strong perfume that is much esteemed by perfumers and some oriental religious communities. The production of agarwood is presumed to depend on environmental factors, among them fungi. The aim of this work is to obtain an overview of fungi present in Aquilaria sp. from different countries. Aquilaria sp. is endemic to South East Asia including notably Cambodia, Laos and Thailand, where it is cultivated to produce agarwood. In French Guiana, farmers would like to locally produce agarwood in their field. That's why we wonder if fungal communities naturally present in French Guiana present characteristics making it compatible with the induction of agarwood. In this study, NGS was used to characterize fungal communities associated with agarwood: 693,961 sequences that cover ITS2 estimated about 250bp have been obtained. These sequences have been grouped into 535 OTUs, displaying 100% identity. In this study, 87% were Ascomycetes and 10.5% were Basidiomycetes. These results show also differences in fungal communities between aboveground and belowground parts of the tree. Likewise, differences between countries within fungal communities were also observed.